From 73efba37dfcab3f9b8589cb3b0b80f6d7dd7bd0b Mon Sep 17 00:00:00 2001 From: cjamin Date: Wed, 4 Oct 2017 10:24:04 +0000 Subject: Document utilies in README files using Markdown + move/rename some utilities Only missing doc for now: Garland_heckbert git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2752 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7ba0113762b6622130835dc9e372acfae29c2db8 --- src/Witness_complex/example/CMakeLists.txt | 21 ++- .../example/example_strong_witness_complex_off.cpp | 79 ++++++++++ .../example_witness_complex_persistence.cpp | 171 --------------------- 3 files changed, 88 insertions(+), 183 deletions(-) create mode 100644 src/Witness_complex/example/example_strong_witness_complex_off.cpp delete mode 100644 src/Witness_complex/example/example_witness_complex_persistence.cpp (limited to 'src/Witness_complex/example') diff --git a/src/Witness_complex/example/CMakeLists.txt b/src/Witness_complex/example/CMakeLists.txt index f8527e0f..a8231392 100644 --- a/src/Witness_complex/example/CMakeLists.txt +++ b/src/Witness_complex/example/CMakeLists.txt @@ -14,25 +14,22 @@ install(TARGETS Witness_complex_example_nearest_landmark_table DESTINATION bin) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) add_executable( Witness_complex_example_off example_witness_complex_off.cpp ) add_executable ( Witness_complex_example_sphere example_witness_complex_sphere.cpp ) - - add_executable ( Witness_complex_example_witness_persistence example_witness_complex_persistence.cpp ) - target_link_libraries(Witness_complex_example_witness_persistence ${Boost_PROGRAM_OPTIONS_LIBRARY}) - - if (TBB_FOUND) - target_link_libraries(Witness_complex_example_witness_persistence ${TBB_LIBRARIES}) - endif() + + add_executable( Witness_complex_example_strong_off example_strong_witness_complex_off.cpp ) + target_link_libraries(Witness_complex_example_strong_off) add_test(NAME Witness_complex_example_off_test_torus COMMAND $ "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3") add_test(NAME Witness_complex_example_test_sphere_10 COMMAND $ "10") - add_test(NAME Witness_complex_example_test_torus_persistence - COMMAND $ - "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "-l" "20" "-a" "0.5") - + add_test(NAME Witness_complex_example_strong_off_test_torus + COMMAND $ + "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" "20" "1.0" "3") + install(TARGETS Witness_complex_example_off DESTINATION bin) install(TARGETS Witness_complex_example_sphere DESTINATION bin) - install(TARGETS Witness_complex_example_witness_persistence DESTINATION bin) + install(TARGETS Witness_complex_example_strong_off DESTINATION bin) + endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0) diff --git a/src/Witness_complex/example/example_strong_witness_complex_off.cpp b/src/Witness_complex/example/example_strong_witness_complex_off.cpp new file mode 100644 index 00000000..0ee9ee90 --- /dev/null +++ b/src/Witness_complex/example/example_strong_witness_complex_off.cpp @@ -0,0 +1,79 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Siargey Kachanovich + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#include +#include +#include +#include + +#include + +#include +#include +#include +#include +#include + +using K = CGAL::Epick_d; +using Point_d = typename K::Point_d; +using Witness_complex = Gudhi::witness_complex::Euclidean_strong_witness_complex; +using Point_vector = std::vector; + +int main(int argc, char * const argv[]) { + if (argc != 5) { + std::cerr << "Usage: " << argv[0] + << " path_to_point_file number_of_landmarks max_squared_alpha limit_dimension\n"; + return 0; + } + + std::string file_name = argv[1]; + int nbL = atoi(argv[2]), lim_dim = atoi(argv[4]); + double alpha2 = atof(argv[3]); + clock_t start, end; + Gudhi::Simplex_tree<> simplex_tree; + + // Read the point file + Point_vector point_vector, landmarks; + Gudhi::Points_off_reader off_reader(file_name); + if (!off_reader.is_valid()) { + std::cerr << "Strong witness complex - Unable to read file " << file_name << "\n"; + exit(-1); // ----- >> + } + point_vector = Point_vector(off_reader.get_point_cloud()); + + std::cout << "Successfully read " << point_vector.size() << " points.\n"; + std::cout << "Ambient dimension is " << point_vector[0].dimension() << ".\n"; + + // Choose landmarks + Gudhi::subsampling::pick_n_random_points(point_vector, nbL, std::back_inserter(landmarks)); + + // Compute witness complex + start = clock(); + Witness_complex witness_complex(landmarks, + point_vector); + + witness_complex.create_complex(simplex_tree, alpha2, lim_dim); + end = clock(); + std::cout << "Strong witness complex took " + << static_cast(end - start) / CLOCKS_PER_SEC << " s. \n"; + std::cout << "Number of simplices is: " << simplex_tree.num_simplices() << "\n"; +} diff --git a/src/Witness_complex/example/example_witness_complex_persistence.cpp b/src/Witness_complex/example/example_witness_complex_persistence.cpp deleted file mode 100644 index a1146922..00000000 --- a/src/Witness_complex/example/example_witness_complex_persistence.cpp +++ /dev/null @@ -1,171 +0,0 @@ -/* This file is part of the Gudhi Library. The Gudhi library - * (Geometric Understanding in Higher Dimensions) is a generic C++ - * library for computational topology. - * - * Author(s): Siargey Kachanovich - * - * Copyright (C) 2016 INRIA (France) - * - * This program is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -#include -#include -#include -#include -#include - -#include - -#include - -#include -#include -#include // infinity - -using K = CGAL::Epick_d; -using Point_d = K::Point_d; - -using Point_vector = std::vector; -using Witness_complex = Gudhi::witness_complex::Euclidean_witness_complex; -using SimplexTree = Gudhi::Simplex_tree<>; - -using Filtration_value = SimplexTree::Filtration_value; - -using Field_Zp = Gudhi::persistent_cohomology::Field_Zp; -using Persistent_cohomology = Gudhi::persistent_cohomology::Persistent_cohomology; - -void program_options(int argc, char * argv[] - , int & nbL - , std::string & file_name - , std::string & filediag - , Filtration_value & max_squared_alpha - , int & p - , int & dim_max - , Filtration_value & min_persistence); - -int main(int argc, char * argv[]) { - std::string file_name; - std::string filediag; - Filtration_value max_squared_alpha; - int p, nbL, lim_d; - Filtration_value min_persistence; - SimplexTree simplex_tree; - - program_options(argc, argv, nbL, file_name, filediag, max_squared_alpha, p, lim_d, min_persistence); - - // Extract the points from the file file_name - Point_vector witnesses, landmarks; - Gudhi::Points_off_reader off_reader(file_name); - if (!off_reader.is_valid()) { - std::cerr << "Witness complex - Unable to read file " << file_name << "\n"; - exit(-1); // ----- >> - } - witnesses = Point_vector(off_reader.get_point_cloud()); - std::cout << "Successfully read " << witnesses.size() << " points.\n"; - std::cout << "Ambient dimension is " << witnesses[0].dimension() << ".\n"; - - // Choose landmarks from witnesses - Gudhi::subsampling::pick_n_random_points(witnesses, nbL, std::back_inserter(landmarks)); - - // Compute witness complex - Witness_complex witness_complex(landmarks, - witnesses); - - witness_complex.create_complex(simplex_tree, max_squared_alpha, lim_d); - - std::cout << "The complex contains " << simplex_tree.num_simplices() << " simplices \n"; - std::cout << " and has dimension " << simplex_tree.dimension() << " \n"; - - // Sort the simplices in the order of the filtration - simplex_tree.initialize_filtration(); - - // Compute the persistence diagram of the complex - Persistent_cohomology pcoh(simplex_tree); - // initializes the coefficient field for homology - pcoh.init_coefficients(p); - - pcoh.compute_persistent_cohomology(min_persistence); - - // Output the diagram in filediag - if (filediag.empty()) { - pcoh.output_diagram(); - } else { - std::ofstream out(filediag); - pcoh.output_diagram(out); - out.close(); - } - - return 0; -} - - -void program_options(int argc, char * argv[] - , int & nbL - , std::string & file_name - , std::string & filediag - , Filtration_value & max_squared_alpha - , int & p - , int & dim_max - , Filtration_value & min_persistence) { - namespace po = boost::program_options; - - po::options_description hidden("Hidden options"); - hidden.add_options() - ("input-file", po::value(&file_name), - "Name of file containing a point set in off format."); - - Filtration_value default_alpha = std::numeric_limits::infinity(); - po::options_description visible("Allowed options", 100); - visible.add_options() - ("help,h", "produce help message") - ("landmarks,l", po::value(&nbL), - "Number of landmarks to choose from the point cloud.") - ("output-file,o", po::value(&filediag)->default_value(std::string()), - "Name of file in which the persistence diagram is written. Default print in std::cout") - ("max-sq-alpha,a", po::value(&max_squared_alpha)->default_value(default_alpha), - "Maximal squared relaxation parameter.") - ("field-charac,p", po::value(&p)->default_value(11), - "Characteristic p of the coefficient field Z/pZ for computing homology.") - ("min-persistence,m", po::value(&min_persistence)->default_value(0), - "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals") - ("cpx-dimension,d", po::value(&dim_max)->default_value(std::numeric_limits::max()), - "Maximal dimension of the weak witness complex we want to compute."); - - po::positional_options_description pos; - pos.add("input-file", 1); - - po::options_description all; - all.add(visible).add(hidden); - po::variables_map vm; - - po::store(po::command_line_parser(argc, argv). - options(all).positional(pos).run(), vm); - po::notify(vm); - - if (vm.count("help") || !vm.count("input-file")) { - std::cout << std::endl; - std::cout << "Compute the persistent homology with coefficient field Z/pZ \n"; - std::cout << "of a Weak witness complex defined on a set of input points.\n \n"; - std::cout << "The output diagram contains one bar per line, written with the convention: \n"; - std::cout << " p dim b d \n"; - std::cout << "where dim is the dimension of the homological feature,\n"; - std::cout << "b and d are respectively the birth and death of the feature and \n"; - std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl; - - std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl; - std::cout << visible << std::endl; - std::abort(); - } -} -- cgit v1.2.3